Hello!, I'm new to systems biology, and I was asked to graph the metabolic pathway that is underneath the production of certain a metabolite from a bacterial taxon.
I have a fasta file corresponding to the complete genome of this microorganism so I used gapseq to predict the full metabolic network of this genome. Now I want to know if is there any tool/tutorial that you can recommend for me to extract the specific pathway related to my metabolite of interest and graph it in R or Python.
By far, I have gapseq outputs that corresponds to tables of predicted pathways (.tbl file) and the final emtabolic network saved in a xml file.
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v.berriosfarias •
1 answer
I am not sure how helpful my response will be as I am in same situation like yours, but..
Did you already try using BigMec - Biosynthetic Gene cluster Metabolic pathway Constructor with antiSMASH output and visualise pathway json file using tools like Escher or Cytoscape ?
Escher maps have options to load JSON and pathway models but unfortunately didn't work in my case.
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